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@sanger-tol

Tree of Life programme

The Tree of Life Programme investigates the diversity of complex organisms (eukaryotes) through sequencing and cellular technology
README.md

Hello 👋 !

You can find here most of the production code used by the Tree of Life 🌍 programme at the Sanger Institute, including the suite of Nextflow pipelines ⚙️ we use to generate hundreds of high-quality reference genome assemblies.

We also use these organisations and repositories:

Visit our main website at https://pipelines.tol.sanger.ac.uk/ to learn more about our mission 🧑‍🚀 !

Popular repositories Loading

  1. PretextView PretextView Public

    OpenGL Powered Pretext Contact Map Viewer

    C 27 7

  2. genomenote genomenote Public

    This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

    Python 24 6

  3. treeval treeval Public

    Pipelines for the production of Treeval data

    Nextflow 22 4

  4. PretextMap PretextMap Public

    Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.

    C 20 2

  5. genomeassembly genomeassembly Public

    Implementation of ToL genome assembly workflows

    Nextflow 20 2

  6. yahs yahs Public

    Forked from c-zhou/yahs

    Yet another Hi-C scaffolding tool

    C 19 3

Repositories

Showing 10 of 45 repositories
  • PretextGraph Public

    Embeds bedgraph data into Pretext contact maps.

    sanger-tol/PretextGraph’s past year of commit activity
    C++ 0 2 0 0 Updated Oct 22, 2024
  • zippypretext Public

    A pipeline that reuses previously generated Hi-C map data to create a new Hi-C map based on a new assembly structure.

    sanger-tol/zippypretext’s past year of commit activity
    1 MIT 0 0 0 Updated Oct 21, 2024
  • ear Public

    ERGA Assembly Report pipeline

    sanger-tol/ear’s past year of commit activity
    Nextflow 0 MIT 0 1 0 Updated Oct 21, 2024
  • blobtoolkit Public

    Nextflow pipeline for BlobToolKit for Sanger ToL production suite

    sanger-tol/blobtoolkit’s past year of commit activity
    Nextflow 11 MIT 2 5 1 Updated Oct 21, 2024
  • agp-tpf-utils Public

    Code for manipulating AGP and TPF assembly files

    sanger-tol/agp-tpf-utils’s past year of commit activity
    Python 2 MIT 1 3 0 Updated Oct 18, 2024
  • readmapping Public

    Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.

    sanger-tol/readmapping’s past year of commit activity
    Nextflow 9 MIT 6 13 3 Updated Oct 18, 2024
  • ascc Public

    A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.

    sanger-tol/ascc’s past year of commit activity
    Python 3 MIT 0 10 1 Updated Oct 17, 2024
  • MicroFinder Public

    order a FASTA file by microchromosome specific genes

    sanger-tol/MicroFinder’s past year of commit activity
    Ruby 2 MIT 1 0 0 Updated Oct 16, 2024
  • singularity-hpc Public Forked from singularityhub/singularity-hpc

    Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.

    sanger-tol/singularity-hpc’s past year of commit activity
    Python 0 MPL-2.0 28 1 0 Updated Oct 15, 2024
  • nf-core-tools Public Forked from nf-core/tools

    Python package with helper tools for the nf-core community.

    sanger-tol/nf-core-tools’s past year of commit activity
    Python 0 MIT 188 4 2 Updated Oct 14, 2024
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